TB-Profiler result

Run: SRR25827702
Summary

Run ID: SRR25827702

Sample name:

Date: 2024-10-04T19:57:31.933150

Number of reads: 15434392

Percentage reads mapped: 99.27

Median coverage: 514.0

Strain: lineage2.2.1;lineage3.1.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.25
lineage3.1.2 East-African-Indian RD750 0.25
lineage2 East-Asian RD105 0.75
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.73
lineage2.2 East-Asian (Beijing) RD105;RD207 0.73
lineage3.1 East-African-Indian RD750 0.25
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Leu Assoc w R
p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Leu Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Gly132Ala Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
gid p.Tyr22* Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
clofazimine mmpR5 c.421_424dupGATC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.421_424dupGATC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpoB 761140 p.His445Leu missense_variant 0.27 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.74 rifampicin Assoc w R
mmpR5 779409 c.421_424dupGATC frameshift_variant 0.72 bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
rpsL 781687 p.Lys43Arg missense_variant 0.75 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.73 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288847 p.Gly132Ala missense_variant 0.72 pyrazinamide Assoc w R
embB 4247429 p.Met306Leu missense_variant 0.23 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.75 ethambutol Assoc w R
gid 4408137 p.Tyr22* stop_gained 0.27 streptomycin Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7581 p.Asp94Arg missense_variant 0.31 levofloxacin
moxifloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.73 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575025 c.-323C>T upstream_gene_variant 0.23 isoniazid
ethionamide
mshA 575907 p.Ala187Val missense_variant 0.73 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.77 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.68 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.25 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.29 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764840 p.Ile491Val missense_variant 0.73 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.74 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.72 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.77 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417933 c.-586G>T upstream_gene_variant 0.26 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.71 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.26 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.27 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.24 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.21 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.27 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2752c 3066462 c.-271G>A upstream_gene_variant 0.29 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.73 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.73 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.25 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.25 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.71 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.26 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.75 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.17 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.76 ethambutol Not assoc w R
aftB 4268753 c.84T>G synonymous_variant 0.75 ethambutol Not assoc w R - Interim
ethA 4327212 p.Thr88Ala missense_variant 0.74 ethionamide
ethA 4327292 p.Thr61Arg missense_variant 0.28 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.73 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.74 streptomycin Not assoc w R